Chemistry 565 / 665 BIOPHYSICAL CHEMISTRY - Spring 2003 - LECTURE: LECTURER: OFFICE HOURS: 9:55 10:45 a.m. MTRF, B383 Chemistry Prof. Silvia Cavagnero Office: 8108 New Chemistry Building (will be 5341 Daniels Chemistry Building) Phone: 262-5430 Email: cavagner@chem.wisc.edu M, R 11:00-11:50 a.m. and by appointment TEACHING ASSISTANT: Eric Fulmer Office: 8131 New Chem. Bldg. (will be 5365 Daniels Chemistry Building) Phone: 265-7948 Email: fulma55@hotmail.com TA OFFICE HOURS: COURSE WEB SITE: M, F 2:00 3:00 p.m. and by appointment genchem.chem.wisc.edu/physical/cavagnero/pcourse.asp You can either type the above or get to the course web site by following this path: www.chem.wisc.edu Education Course Pages Current Courses BIOPHYSICAL CHEMISTRY WEB SITE: http://www.library.wisc.edu/libraries/chemistry/biophysics /biophysicshome.htm INTRODUCTION Chemistry 565 / 665 is an introductory class on equilibrium thermodynamics and chemical kinetics with emphasis to biological applications. Issues of particular interest are the concept of entropy, enthalpy and free energy, the kinetics of complex reactions, the non covalent forces that determine protein and nucleic acid stability (particularly the hydrophobic effect, electrostatic interactions and the hydrogen bond) and the folding and misfolding kinetics of proteins and nucleic acids. TEXTBOOK AND OTHER REQUIRED MATERIAL - 1 -
1. Dill & Bromberg, Molecular Driving Forces, Garland Science, 2003. 2. An inexpensive calculator. It should have capabilities for square roots, logarithms and exponential operations. The calculator will be used on exams and homework assignments. A programmable calculator will not be allowed during exams. ADDITIONAL USEFUL READING Handouts distributed in class; Tinoco, Sauer, Wang and Puglisi, Physical Chemistry: Principles and Applications in Biological Sciences, Pearson Education, 2001; Van Holde, Johnson and Ho, Principles of Physical Biochemistry, Prentice Hall, 1998; Hammes, Themodynamics and Kinetics for the Biological Sciences, Wiley& Sons, 2000; Connors, Chemical Kinetics, The study of Reaction Rates in Solution, VCH, 1990; Fersht, Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Freeman, 1999; Daune, Molecular Biophysics: Structures in Motion, Oxford Un. Press, 1999; Eisenberg and Crothers, Physical Chemistry with Applications to the Life Sciences, Addison- Wesley, 1979; Cantor and Schimmel, Biophysical Chemistry, Parts 1, 2 and 3, Freeman, 1980; Klotz and Rosenberg, Chemical Thermodynamics, Wiley & Sons, 1994; Jencks, Catalysis in Chemistry and Enzymology, Wiley & Sons, 1975; Klotz, Ligand-Receptor Energetics, Wiley & Sons, 1997; Weber, Protein Interactions, Chapman & Hall, 1992; Espenson, Chemical Kinetics and Reaction Mechanisms, Mc Graw Hill, 1995; Creighton, Proteins: Structures and Molecular Properties, Freeman & Co., 1992; Crothers, Bloomfield, Tinoco, Nucleic Acids, Structures, Properties and Functions, University Science Books, 2000; Nelson and Cox, Lehninger Principles of Biochemistry, Worth, 2000; Stryer, Biochemistry, Freeman, 1995. COURSE INFORMATION Lectures. During lectures we will discuss principles, and illustrate them with examples. You should take your own notes during lecture. In addition, a set of lecture notes taken by a Teaching Assistant (TA) will be available on the web (see course website above). Lecture Schedule. The Biophysical Chemistry (Chem 565/665) lectures are on Mondays, Tuesdays, Thursdays and Fridays at 9:55 am. Please check the course outline (which follows) for a detailed schedule of the lectures. Textbook. The textbook supplements the lectures. It provides background material for the lectures and also works out many relevant examples. In addition, at the end of each chapter are a number of problems. For an understanding of the material in this course it is important to solve as many of these problems as possible. Plan to buy your own textbook. A reference copy of the textbook is available for consultation in the Chemistry library. This library also contains a copy of the Additional Useful Reading material listed above. - 2 -
Problems. For each chapter a set of especially relevant problems is assigned. The formation of study groups for working on problems is strongly encouraged. Difficulties with any problems should be discussed with your TA in the discussion sections. Your solutions to the problems are due in the TA mailbox on selected Mondays by 5 p.m. (see detailed schedule below). The problems will be graded by your TA. Answer Keys to the problems will be distributed during Discussion Sections on Wednesdays. Discussion Section. Discussion sections are primarily for review and problem solving relevant to the recent lecture material. Your TA will go over some examples similar to the assigned problems. You should be prepared when you come to discussion section. Ask specific questions to your TA and plan to be interactive. Exams. There will be two two-hour exams, one class presentation on a special topic in biophysical chemistry related to the course, and a two-hour final exam. Check the course outline (which follows) for the examination dates and times. The exams will primarily be based on the material presented in the lectures, and on material illustrated by the assigned problems. No make-up exams will be given. The final exam will be comprehensive, covering topics from the entire semester. Oral Presentation. All students will independently work on a well defined special topic in biophysical chemistry of their choice. Example of possible special topics are: polymer dynamics, the hydrophobic effect, helix-coil transition theory, cooperative processes in biology, the effect of pressure on protein stability, ion pairs in biology, design of proteins with a desired fold and function, the thermodynamic effects of denaturing agents, secondary vs tertiary structure formation in protein folding, the diffusion-collision protein folding model, the Flory-Huggins model and its predictions on polymer behavior, the hydrophobic zipper protein folding model, the kinetics of hydrophobic collapse, water and its role in biology, protein folding landscapes: theory and experiments, mechanisms and kinetics of polypeptide aggregation, and so on. Plan to talk to Prof. Cavagnero well in advance to discuss your choice of special topic. The special topic will be presented to the class during the last two weeks of class according to the class schedule below. Either transparencies or a powerpoint presentation are recommended. A hard copy of your presentation panels is due to the teacher. Students taking the course as Chem 665 are also expected to write a short report on their special topic of choice. Biophysical Chemistry Website. This web site contains a lot of valuable educational information on various areas of biophysical chemistry. Use it as a personal resource for learning more about this exciting field. This site also contains a collection of valuable database information for researchers involved in the biophysics field. A selected number of assigned homework problems will involve using this web site. Grades. This course will be graded on a maximum of 100 points divided as follows: Exam I Exam II 20 points 20 points - 3 -
Special Topic Presentation Homework Questions Final Exam Total 10 points 20 points 30 points 100 points Your course grade will be determined by the total number of points you have accumulated. COURSE OUTLINE DATE TOPIC CHAPTER NOTES ON PROBLEM SETS T Jan 21 Principles of Probability 1 R Jan 23 Principles of Probability 1 F Jan 24 Principles of Probability 1 Problem Set #1 Assigned and Biophys. Chem. Website Presentation by Emily Wixson M Jan 27 Predicting Equilibrium in 2 Chemistry and Biology T Jan 28 Predicting Equilibrium in 2 Chemistry and Biology R Jan 30 Heat, Work & Energy 3 F Jan 31 Heat, Work & Energy 3 M Feb 3 Math Tools 4 Problem Set #1 Due T Feb 4 Math Tools 4 R Feb 6 TA Lecture on Problem Solving -- F Feb 7 TA Lecture on Problem Solving -- Problem Set #2 Assigned M Feb 10 Multivariate Calculus 5 T Feb 11 Multivariate Calculus 5 R Feb 13 Entropy & the Boltzmann Distr. Law 6 F Feb 14 Entropy & the Boltzmann Distr. Law 6-4 -
M Feb 17 Entropy & the Boltzmann Distr. Law 6 Problem Set #2 Due T Feb 18 Thermodynamic Driving Forces 7 R Feb 20 Thermodynamic Driving Forces 7 F Feb 21 Thermodynamic Driving Forces 7 Problem Set #3 Assigned M Feb 24 Thermodynamic Driving Forces 7 T Feb 25 Free Energies 8 R Feb 27 Free Energies 8 F Feb 28 Free Energies 8 Problem Set #4 Assigned M Mar 3 Maxwell s Relations and Mixtures 9 Problem Set #3 Due T Mar 4 Maxwell s Relations and Mixtures 9 R Mar 6 The Boltzmann Distribution Law 10 F Mar 7 The Boltzmann Distribution Law 10 M Mar 10 The Boltzmann Distribution Law 10 Problem Set #4 Due T Mar 11 TA Lecture on Problem Solving -- R Mar 13 Review Lecture -- F Mar 14 Exam I (5:30 7:30 pm, room TBA)-- M Mar 17 Spring Recess - No Lecture -- T Mar 18 Spring Recess - No Lecture -- R Mar 20 Spring Recess - No Lecture -- F Mar 21 Spring Recess - No Lecture -- M Mar 24 Temperature and Heat Capacity 12 T Mar 25 Temperature and Heat Capacity 12 R Mar 27 Temperature and Heat Capacity 12-5 -
F Mar 28 Chemical Equilibria 13 Problem Set #5 Assigned M Mar 31 Chemical Equilibria 13 T Apr 1 Heat Capacity and Protein Stability -- R Apr 3 Equilibria between Liquids, 14 Solids & Gases F Apr 4 Equilibria between Liquids, 14 Solids & Gases M Apr 7 Solutions and Mixtures 15 Problem Set #5 Due T Apr 8 Solutions and Mixtures 15 R Apr 10 Solvation and Phase Transfer 16 F Apr 11 Solvation and Phase Transfer 16 Problem Set #6 Assigned M Apr 14 Vector Calculus 17 T Apr 15 Physical Kinetics 18 R Apr 17 Physical Kinetics 18 F Apr 18 Physical Kinetics 18 Problem Set #7 Assigned M Apr 21 Chemical Kinetics & Transition 19 Problem Set #6 Due States T Apr 22 Chemical Kinetics & Transition 19 States R Apr 24 Chemical Kinetics & Transition 19 States F Apr 25 Energy Landscapes & Protein -- Problem Set #7 Due Folding Kinetics M Apr 28 Review Lecture -- T Apr 29 Exam II (5:30 7:30 pm, room TBA) -- R May 1 Student Oral Presentations -- - 6 -
F May 2 Student Oral Presentations -- M May 5 Student Oral Presentations -- T May 6 Student Oral Presentations -- R May 8 Student Oral Presentations -- F May 9 Student Oral Presentations -- R May 15 FINAL EXAM (12:25 2:25 pm, room TBA) - 7 -